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Maizatul-Suriza M, Dickinson M, Al-Jaf B, Madihah AZ. Cross-pathogenicity of Phytophthora palmivora associated with bud rot disease of oil palm and development of biomarkers for detection. World J Microbiol Biotechnol 2024; 40:55. [PMID: 38165501 DOI: 10.1007/s11274-023-03860-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
Phytophthora palmivora has caused disease in many crops including oil palm in the South America region. The pathogen has had a significant economic impact on oil palm cultivation in Colombia, and therefore poses a threat to oil palm cultivation in other regions of the World, especially in Southeast Asia, the largest producer of the crop. This study aimed to look at the ability of isolates from Malaysia, Colombia, and other regions to cross-infect Malaysian oil palm, durian, and cocoa and to develop specific biomarkers and assays for identification, detection, and diagnosis of P. palmivora as a key component for the oil palm biosecurity continuum in order to contain the disease especially at the ports of entry. We have developed specific molecular biomarkers to identify and detect Phytophthora palmivora using polymerase chain reaction (PCR) and real-time loop mediated isothermal amplification (rt-LAMP) in various sample types such as soil and plants. The limit of detection (DNA template, pure culture assay) for the PCR assay is 5.94 × 10-2 ng µl-1 and for rt-LAMP is 9.28 × 10-4 ng µl-1. Diagnosis using rt-LAMP can be achieved within 30 min of incubation. In addition, PCR primer pair AV3F/AV3R developed successfully distinguished the Colombian and Malaysian P. palmivora isolates.
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Affiliation(s)
- Mohamed Maizatul-Suriza
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, Leicestershire, UK.
| | - Matthew Dickinson
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, Leicestershire, UK
| | - Bryar Al-Jaf
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, Leicestershire, UK
- Horticulture Department, College of Agricultural Engineering Sciences, University of Sulaimani, Sulaimani, Iraq
| | - Ahmad Zairun Madihah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
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Leiva AM, Pardo JM, Arinaitwe W, Newby J, Vongphachanh P, Chittarath K, Oeurn S, Thi Hang L, Gil-Ordóñez A, Rodriguez R, Cuellar WJ. Ceratobasidium sp. is associated with cassava witches' broom disease, a re-emerging threat to cassava cultivation in Southeast Asia. Sci Rep 2023; 13:22500. [PMID: 38110543 PMCID: PMC10728180 DOI: 10.1038/s41598-023-49735-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Cassava witches' broom disease (CWBD) is a devastating disease of cassava in Southeast Asia (SEA), of unknown etiology. Affected plants show reduced internodal length, proliferation of leaves and weakening of stems. This results in poor germination of infected stem cuttings (i.e., planting material) and significant reductions in fresh root yields and starch content, causing economic losses for farmers and processors. Using a metagenomic approach, we identified a fungus belonging to the Ceratobasidium genus, sharing more than 98.3-99.7% nucleotide identity at the Internal Transcribed Spacer (ITS), with Ceratobasidium theobromae a pathogen causing similar symptoms in cacao. Microscopy analysis confirmed the identity of the fungus and specific designed PCR tests readily showed (1) Ceratobasidium sp. of cassava is strongly associated with CWBD symptoms, (2) the fungus is present in diseased samples collected since the first recorded CWBD outbreaks in SEA and (3) the fungus is transmissible by grafting. No phytoplasma sequences were detected in diseased plants. Current disease management efforts include adjustment of quarantine protocols and guarantee the production and distribution of Ceratobasidium-free planting material. Implications of related Ceratobasidium fungi, infecting cassava, and cacao in SEA and in other potential risk areas are discussed.
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Affiliation(s)
- Ana M Leiva
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Juan M Pardo
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Warren Arinaitwe
- Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cassava Program Asia Office, P.O. Box 783, Vientiane, Lao PDR
| | - Jonathan Newby
- Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cassava Program Asia Office, P.O. Box 783, Vientiane, Lao PDR
| | - Pinkham Vongphachanh
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, P.O. Box 811, Vientiane, Lao PDR
| | - Khonesavanh Chittarath
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, P.O. Box 811, Vientiane, Lao PDR
| | - Samoul Oeurn
- Plant Protection Sanitary and Phytosanitary Department, General Directorate of Agriculture (GDA), Phnom Penh, 120406, Cambodia
| | - Le Thi Hang
- Plant Protection Research Institute (PPRI), Duc Thang Bac Tu Liem, Hanoi, 100000, Vietnam
| | - Alejandra Gil-Ordóñez
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Rafael Rodriguez
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Wilmer J Cuellar
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia.
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Li Z, Wang Z, Lu S, Yu D, Chen Q. Identification and First Report of Leaf Blight Caused by Phytophthora palmivora on Chinese Water Bamboo in China. PLANT DISEASE 2022; 107:588. [PMID: 35802016 DOI: 10.1094/pdis-05-22-1180-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chinese water bamboo (Dracaena sanderiana) is a popular houseplant due to its ability to survive in various indoor conditions. In October 2020, pronounced leaf blight symptoms with approximately 50% disease incidence were observed on water bamboo in the 35-ha field of Wenchang county (19°50'45'' N, 110°21'38'' E), Hainan, China. The diseased leaves showed pale green with yellowish lesions, dried and shrivelled tips. As the disease progressed, upward-spreading necrosis led to stem weakness, and then the plants wilted and died within a few weeks (Fig. 1A,B). Ten symptomatic leaves were collected, and leaf pieces (5 mm × 5 mm) from the edge of the lesion were cut, disinfected for 30 s using 75% ethanol, and rinsed five times in d.d. H2O, and placed on V8 media amended with 10 mg/L pimaricin, 150 mg/L ampicillin, and 16 mg/L rifampicin (Guo et al., 2012). Eight isolates of Phytophthora recovered from 10 leaves were characterized morphologically. Colony morphology showed slightly radiate to stellate patterns, with cottony aerial mycelium (Fig.1D). Hyphae were smooth and uniform, branching at nearly right angles into stout (Fig.1E). Mycelial swellings were observed in plate culture (Fig.1F). Chlamydospores were abundant and spherical (Fig.1G). Sporangia were produced externally through sympodial development of the sporangiophore immediately below a sporangium (Fig.1H, I). The sporangia were 29.3-63.9 µm (mean, 48.5 µm) in length and 19.3-46.8 µm (mean, 33.5 µm, n=50) in width. No sexual organs were observed in the 8 isolates. The morphological characteristics of the isolates were consistent with the description of P. palmivora (Erwin and Ribeiro, 1996). The internal transcribed spacer (ITS) region of rDNA, the translation elongation factor 1α gene (TEF1), and β-Tubulin gene (TUB) sequences of the 8 isolates were amplified using the primers ITS1/ITS4 (Cooke et al., 2000), ELONGF1/ELONGR1 and TUBUF2/TUBUR1 (Kroon, et al., 2004), respectively, followed by sequencing analysis. The sequences of representative isolate HK-5 for the ITS, TEF1 and TUB were deposited in GenBank with the accession numbers of OK349485, OK349488 and OK349487. BLAST results showed that the ITS (MG865559, identity=735/735; 100%), TEF1(MH359047, identity=682/684; 99.7%) and TUB (MH493992, identity=467/468; 99.8%) sequences were all highly similar with a sequence of P. palmivora strain CPHST BL105. Phylogenetic analysis using the combined ITS, TEF1, and TUB sequences showed that the isolate HK-5 were grouped with the P. palmivora with good bootstrap support (Fig.2). Based on morphological and molecular identification, the pathogens were identified as P. palmivora. The pathogenicity tests showed that all whole plants (1-year-old) sprayed with the 5 mL of zoospore suspension (1×106 zoospores mL-1) initially presented with discoloured spots on their leaves after 4 days of inoculation, and the symptoms gradually progressed from spots to leaf blight (Fig. 1C). Each isolate was applied onto 10 plants and control plants were sprayed with d.d.H2O. The results of the pathogenicity test exhibited typical symptoms as observed in the field. No significant differences of virulence were observed among the 8 isolates, and the control plants remained symptomless. P. palmivora was re-isolated from the leaves of inoculated plants. This is the first report of P. palmivora on water bamboo in China, and appropriate measures must be undertaken to control this agent in this region.
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Affiliation(s)
- Zhiting Li
- Hainan University, 74629, Haikou, Hainan, China;
| | - Zhixin Wang
- Hainan University, 74629, plant protection, hainan university, Haikou, China, 570288;
| | - Shengdan Lu
- Hainan University, 74629, Haikou, Hainan, China;
| | - Dan Yu
- Hainan University, 74629, Haikou, Hainan, China;
| | - Qinghe Chen
- Hainan University, 74629, Plant Pathology, 58 Renmin Avenue, Haikou, Hainan, China, 570288
- Fujian Academy of Agricultural Sciences, 107629, Plant Pathology, 247 Wusi Rd., Fuzhou, China, 350003;
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Guo Y, Sakalidis ML, Torres-Londono GA, Hausbeck MK. Population Structure of a Worldwide Phytophthora palmivora Collection Suggests Lack of Host Specificity and Reduced Genetic Diversity in South America and the Caribbean. PLANT DISEASE 2021; 105:4031-4041. [PMID: 33983798 DOI: 10.1094/pdis-05-20-1055-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytophthora palmivora (Butler) is a highly destructive plant pathogen that infects tropical hosts worldwide, many of which are economically important crops. Despite the broad host range and wide distribution, the pathogen has displayed a considerable amount of variation in morphological characters, including virulence. However, the genetic variability at a global level, which is critical to understand the center of origin and the potential pathway(s) of introduction, was unclear. Here, we mapped the genetic variation of P. palmivora using isolates representing four regions, 15 countries, and 14 host species. We designed a large set of simple sequence repeat markers from the P. palmivora genome and picked 17 selectively neutral markers to screen 98 P. palmivora isolates. We found that P. palmivora populations from our collection generally did not cluster according to host; rather, some isolates from North America were generally distinct from all other populations. Isolates from South America and the Caribbean clustered and appeared to share ancestry with isolates from Asia. Populations from North America and Asia were the most genetically diverse, while the South American and Caribbean populations exhibited similar reduced genetic diversity. The isolates collected in various plantations in Colombia did not show host or geographic specificity. Our study brought a further understanding of this important plant pathogen, although the determination for hypothesized source of origin, spread, and evolution would need further sampling. The genomic resources developed in this study would facilitate further studies on P. palmivora diagnostics and management.
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Affiliation(s)
- Yufang Guo
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Monique L Sakalidis
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
- Department of Forestry, Michigan State University, East Lansing, MI 48824
| | | | - Mary K Hausbeck
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
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Han X, Shen D, Xiong Q, Bao B, Zhang W, Dai T, Zhao Y, Borriss R, Fan B. The Plant-Beneficial Rhizobacterium Bacillus velezensis FZB42 Controls the Soybean Pathogen Phytophthora sojae Due to Bacilysin Production. Appl Environ Microbiol 2021; 87:e0160121. [PMID: 34550751 PMCID: PMC8580012 DOI: 10.1128/aem.01601-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Soybean root rot caused by the oomycete Phytophthora sojae is a serious soilborne disease threatening soybean production in China. Bacillus velezensis FZB42 is a model strain for Gram-positive plant growth-promoting rhizobacteria and is able to produce multiple antibiotics. In this study, we demonstrated that B. velezensis FZB42 can efficiently antagonize P. sojae. The underlying mechanism for the inhibition was then investigated. The FZB42 mutants deficient in the synthesis of lipopeptides (bacillomycin D and fengycin), known to have antifungal activities, and polyketides (bacillaene, difficidin, and macrolactin), known to have antibacterial activities, were not impaired in their antagonism toward P. sojae; in contrast, mutants deficient in bacilysin biosynthesis completely lost their antagonistic activities toward P. sojae, indicating that bacilysin was responsible for the activity. Isolated pure bacilysin confirmed this inference. Bacilysin was previously shown to be antagonistic mainly toward prokaryotic bacteria rather than eukaryotes. Here, we found that bacilysin could severely damage the hyphal structures of P. sojae and lead to the loss of its intracellular contents. A device was invented allowing interactions between P. sojae and B. velezensis FZB42 on nutrient agar. In this manner, the effect of FZB42 on P. sojae was studied by transcriptomics. FZB42 significantly inhibited the expression of P. sojae genes related to growth, macromolecule biosynthesis, pathogenicity, and ribosomes. Among them, the genes for pectate lyase were the most significantly downregulated. Additionally, we showed that bacilysin effectively prevents soybean sprouts from being infected by P. sojae and could antagonize diverse Phytophthora species, such as Phytophthora palmivora, P. melonis, P. capsici, P. litchi, and, most importantly, P. infestans. IMPORTANCEPhytophthora spp. are widespread eukaryotic phytopathogens and often extremely harmful. Phytophthora can infect many types of plants important to agriculture and forestry and thus cause large economic losses. Perhaps due to inappropriate recognition of Phytophthora as a common pathogen in history, research on the biological control of Phytophthora is limited. This study shows that B. velezensis FZB42 can antagonize various Phytophthora species and prevent the infection of soybean seedlings by P. sojae. The antibiotic produced by FZB42, bacilysin, which was already known to have antibacterial effectiveness, is responsible for the inhibitory action against Phytophthora. We further showed that some Phytophthora genes and pathways may be targeted in future biocontrol studies. Therefore, our data provide a basis for the development of new tools for the prevention and control of root and stem rot in soybean and other plant diseases caused by Phytophthora.
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Affiliation(s)
- Xingshan Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Dongxia Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Beihua Bao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenbo Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Tingting Dai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yinjuan Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, Greifswald, Germany
| | - Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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Fones HN, Bebber DP, Chaloner TM, Kay WT, Steinberg G, Gurr SJ. Threats to global food security from emerging fungal and oomycete crop pathogens. ACTA ACUST UNITED AC 2020; 1:332-342. [PMID: 37128085 DOI: 10.1038/s43016-020-0075-0] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 04/09/2020] [Indexed: 11/09/2022]
Abstract
Emerging fungal and oomycete pathogens infect staple calorie crops and economically important commodity crops, thereby posing a significant risk to global food security. Our current agricultural systems - with emphasis on intensive monoculture practices - and globalized markets drive the emergence and spread of new pathogens and problematic traits, such as fungicide resistance. Climate change further promotes the emergence of pathogens on new crops and in new places. Here we review the factors affecting the introduction and spread of pathogens and current disease control strategies, illustrating these with the historic example of the Irish potato famine and contemporary examples of soybean rust, wheat blast and blotch, banana wilt and cassava root rot. Our Review looks to the future, summarizing what we see as the main challenges and knowledge gaps, and highlighting the direction that research must take to face the challenge of emerging crop pathogens.
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